When the league was formed in the late 1800s, association football was just beginning to gather popularity in England. The Football League itself had only begun nine years before the York League, it was also founded prior to the city's now primary team York City. Upon the league's formation, nine teams entered into the league, the founding clubs were:

Throughout the league's history, the only club from the first ever season to continue in an unbroken existence are Rowntrees (now known as Nestlé Rowntree) until their demise at the start of the 2013–14 season.

However, Bishopthorpe United, Easingwold Town and St. Clements are at present still playing in the York League system, after refounding at various points.

Acomb and Rowntrees (along with fellow league team, York YMCA) also went on to become founding members of the Yorkshire League for the 1920–21 season.[2]

Today it has a total of five divisions (and three reserve divisions) including the York League Premier Division which sits at level 11 of the English football league system. The league title has been regularly changing with no team retaining its since 2007–08 when Huntington Rovers achieved it. A number of teams that have recently joined the league have progressed successfully though the divisions to the Premier Division (Tadcaster Magnets, F1 Racing and Sporting Knavesmire).

New teams entering for the 2017-18 season are Clifford, Elm Bank, Stillington and Wistow.

Below is an incomplete list of previous champions at the second level of York League football. From 1923 until 1960 (with the exception of 1932–33, 1939–40 and 1946–47), this division was split into two groups, hence why for those years there are two champions.

Below is an incomplete list of previous champions at the third level of York League football. The most common structure for the league was where it was split into two groups at the same level, hence the reason for two champions in some seasons. At times there were even three groups under the same league at this level.